Sci Ed SoftwareSoftware for the Molecular Biologist

New in Clone Manager 10

Clone Manager 10 is now DPI-aware and can take advantage of your high-resolution screen display.
This means clearer text and better map drawing. In addition, new fonts are being used and a new
color palette has been implemented. To accommodate those with smaller displays (smaller laptops and
2-in1’s in tablet mode), menus are now shorter, toolbars are shorter, and
individual toolbar buttons are larger.

New Licensing Flexibility

With Clone Manager 10, the Individual User license and Small
WorkGroup license classifications have been replaced with a simple Seat
License configuration. Each seat license is installed on a single computer.
You can order as many seat licenses as you need, with volume discount
pricing applied to your order.

Each license is managed on its own computer -- you can activate a
license, transfer it to another computer, or join a concurrent user
group (if you are using the network concurrent version). The new License
Management wizard will assist you with these tasks.

Concurrent-user license management is also easier and more flexible
with Clone Manager 10.
Installation of the licensing service on your network server can be as
simple as possible, or you can use more advanced options to configure
multiple licenses or multiple user groups. There is also a new, smaller
license available (2-user concurrent license) and a fully functional
time-limited evaluation license that will allow you to fully test how
the concurrent license will perform in your environment.

Main toolbar, menu changes

The new main toolbar has some familiar buttons, some new buttons, and
some buttons that have been removed and the functions accessed through the appropriate menu
(Clone, Primer or Align).

A new toolbar section gives easy access to places you may want to visit often:

Molecule List

View list of loaded or newly-created molecules

Primer List

View active/loaded primers and primer collections

Enzyme Lists

View lists of enzymes or create new user lists

Sequence Phrases

View or manage your sequence phrase collection

Data Book

Simple built-in database for molecule information

Add Entry

Add an entry to DataBook or to a primer collection

New easy main toolbar access to Find in Files option. Use this to
scan molecule files to look for certain genes or specific text in the
molecule name or description, or search the Notes field in Clone Manager files (*.cm5).

Ligation Update

The ligation module now supports joining together two or more pieces
of DNA. The new ligate display window shows you the molecules or
fragments as they are being prepared for ligation.

In the upper half of the new window, an icon map of the active
molecule is shown, with features (if any). If enzymes were used to
create the molecule’s ends, these enzyme names appear above the
respective end. The actual sequence of each end is shown below the map.
The molecule in this window can be modified (see below). Use the Fragment Information
button to view the features table for this molecule or to find enzymes that could prepare
ends that would be compatible to the fragment to the left or right (in lower window).

In the lower half of the window, all of the molecules or fragments
are shown in boxes. Click the Add Molecule button to select additional
molecules to add to this window. You should arrange these molecules in
the order in which they should be joined. Click on a molecule and drag
to move to the right or left, as needed. Small icons appear between each
fragment box to indicate if ligation is possible. If changes are needed to a
fragment, click to select the fragment, causing it to appear in the upper box,
where modifications can be made.

Use the Cut Fragment button to access the cut molecule operations for
the selected molecule. You can cut a circular molecule to make it
linear, cut out a region to be cloned, or cut with an enzyme to make a
compatible end. Use the Modify Ends button to access the modify ends operations for
the selected molecule. You can use standard or custom end modifications
to prepare molecule ends for ligation. Use the Invert Fragment button to reverse
(invert) the sequence of the selected molecule. Use the Undo button to undo the
last modification to the selected molecule.

Click the Ligate button to join all compatible ends of the fragments
in the order shown. If you do not want the ligate operation to
circularize the molecule, click on the drop-down arrow to the right on
the Ligate button and select Do not circularize. Once ligation is complete,
you can enter the molecule to the molecule list for further use or save it to disk.

New Cloning Wizards Implemented

The assembly cloning wizards now support Gibson Assembly, In-Fusion
cloning and Ligation-Independent cloning techniques. The wizards will
help you to select the appropriate components, show you the proposed
result, and create the resulting recombinant molecule. Select one of the
assembly cloning wizards from the Clone menu to get started.

Use the Ligation-Independent Cloning wizard to join fragments previously
prepared with correct overlaps. Use the Gibson Cloning or In-Fusion
cloning wizards to use PCR to create amplified fragments with overlaps,
and then assemble the fragments, using the assembly procedure selected.
Set the procedure and primer design options, if applicable.

Click the Create Molecule button to have the program automatically do the
required steps to simulate the cloning experiment, produce the recombinant
molecule, and enter to the Molecule List.

Working Map Update

Working (on-screen) maps now show features in the style and color
selected. Features with joins use a narrow line to connect the joined
segments. The updated color palette produces well-balanced map figures
in contemporary colors. Updated fonts improve feature name and enzyme site text.

Easy, right-click access to customization now includes the ability to
select your three default styles. New toolbar button in map window to create an Enhanced
View map.

Features Table Update

New user settings support displaying feature basepair positions as
left-to-right or start-to-end. And you can now elect to show an iconic
map of the molecule with selected feature highlighted above the table,
and the selected feature map style/color and sequence color below the
table.

The option to show information-only features on the features table is
now included in Settings. New custom settings dialog box for features
makes it easy to use the three default styles, as well as the individual
feature custom settings. You may find it helpful to use style 1 (solids)
for important features, and style 2 (shaded) or style 3 (open) for
less-important features.

Molecule List Update

The molecule list now has the ability to show more information about
the selected molecule. You can see the number of features, primers and
enhanced maps contained within the molecule file, as well as the start
of the Notes field. Use the More Info/Less Info button to show or hide
this information.

BLAST Update

You can now set up a remote search using the NCBI BLAST server with
the new Align, BLAST Search (NCBI REST) option. Results are displayed in
a new table format. (If you prefer, you can still use the legacy
WebBlast (NCBI Browser) option to perform the BLAST search using the
built-in web browser to show the NCBI results data). With either results
view, you can click the Get Molecule button to import the molecule
directly into Clone Manager for use now.